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<div class="title">moltk/dp_params.hpp</div>  </div>
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<a href="dp__params_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment"> * dp_params.hpp</span>
<a name="l00003"></a>00003 <span class="comment"> *</span>
<a name="l00004"></a>00004 <span class="comment"> */</span>
<a name="l00005"></a>00005 
<a name="l00012"></a>00012 <span class="preprocessor">#ifndef MOLTK_DP_PARAMS_HPP_</span>
<a name="l00013"></a>00013 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_DP_PARAMS_HPP_</span>
<a name="l00014"></a>00014 <span class="preprocessor"></span>
<a name="l00015"></a>00015 <span class="keyword">namespace </span>moltk {
<a name="l00016"></a>00016 
<a name="l00022"></a><a class="code" href="namespacemoltk_1_1dp.html">00022</a> <span class="keyword">namespace </span>dp {
<a name="l00023"></a>00023 
<a name="l00024"></a>00024 <span class="comment">// Various options that affect the details of the</span>
<a name="l00025"></a>00025 <span class="comment">// dynamic programming alignment algorithm</span>
<a name="l00026"></a>00026 
<a name="l00028"></a><a class="code" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fe">00028</a> <span class="keyword">enum</span> <a class="code" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fe" title="Fast O(n^2) memory use vs. 2X slower O(n) memory use.">DPMemoryModel</a> {
<a name="l00029"></a><a class="code" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647feab8548c282fd21547171c41cb000859b2">00029</a>     <a class="code" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647feab8548c282fd21547171c41cb000859b2" title="Faster O(n^2) memory model.">DP_MEMORY_LARGE</a>, 
<a name="l00030"></a><a class="code" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fea55075aaaa2895a6d9dd46271a9ca0ab3">00030</a>     <a class="code" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fea55075aaaa2895a6d9dd46271a9ca0ab3" title="2X slower O(n) memory model">DP_MEMORY_SMALL</a> 
<a name="l00031"></a>00031 };
<a name="l00032"></a>00032 
<a name="l00033"></a>00033 
<a name="l00035"></a><a class="code" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8a">00035</a> <span class="keyword">enum</span> <a class="code" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8a" title="Whether alignment operands have preexisting gaps (e.g. alignments) or not (e.g. single sequences)...">DPAlignGapping</a> {
<a name="l00036"></a><a class="code" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8aa19b182379f9aee058d724619e502727c">00036</a>     <a class="code" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8aa19b182379f9aee058d724619e502727c" title="Alignment with no preexisting gaps can be faster and truly optimal.">DP_ALIGN_UNGAPPED_SEQUENCES</a>, 
<a name="l00037"></a><a class="code" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8aad39f6552ff8d735f2b69a72f560d8c90">00037</a>     <a class="code" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8aad39f6552ff8d735f2b69a72f560d8c90" title="Alignment of pregapped sequences is slower and heuristic (problem is NP-hard)">DP_ALIGN_GAPPED_ALIGNMENTS</a> 
<a name="l00038"></a>00038 };
<a name="l00039"></a>00039 
<a name="l00040"></a>00040 
<a name="l00042"></a><a class="code" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4">00042</a> <span class="keyword">enum</span> <a class="code" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4" title="Global vs. local alignment.">DPAlignScale</a> {
<a name="l00043"></a><a class="code" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4af155cf0d0612b514f7738fa8de8735ce">00043</a>     <a class="code" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4af155cf0d0612b514f7738fa8de8735ce" title="Global alignment (Needleman Wunsch)">DP_ALIGN_GLOBAL</a>, 
<a name="l00044"></a><a class="code" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4a42868d0ce46f2b0c694131013b187e0d">00044</a>     <a class="code" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4a42868d0ce46f2b0c694131013b187e0d" title="Local alignment (Smith Waterman)">DP_ALIGN_LOCAL</a>, 
<a name="l00045"></a>00045 };
<a name="l00046"></a>00046 
<a name="l00047"></a>00047 
<a name="l00049"></a><a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0c">00049</a> <span class="keyword">enum</span> <a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0c" title="TracebackPointer to help reconstruct the final alignment.">TracebackPointer</a>
<a name="l00050"></a>00050 {
<a name="l00051"></a><a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0ca9d2fbcded45ce4a53f3dfc4d93ae9f42">00051</a>     <a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0ca9d2fbcded45ce4a53f3dfc4d93ae9f42">TRACEBACK_UPLEFT</a>, <span class="comment">// consume/align one column/residue from each of both alignments/sequences</span>
<a name="l00052"></a><a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0cab17ffddcd5713d8a8d67ebfcff4fccdc">00052</a>     <a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0cab17ffddcd5713d8a8d67ebfcff4fccdc">TRACEBACK_UP</a>, <span class="comment">// consume/delete one column/residue of alignment/sequence 1</span>
<a name="l00053"></a><a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0ca448324d993ba9dd1c87753515d34d6ee">00053</a>     <a class="code" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0ca448324d993ba9dd1c87753515d34d6ee">TRACEBACK_LEFT</a> <span class="comment">// consume/delete one column/residue of alignment/sequence 2</span>
<a name="l00054"></a>00054 };
<a name="l00055"></a>00055 
<a name="l00056"></a>00056 
<a name="l00057"></a>00057 }} <span class="comment">// namespace moltk::dp</span>
<a name="l00058"></a>00058 
<a name="l00059"></a>00059 <span class="preprocessor">#endif </span><span class="comment">/* MOLTK_DP_PARAMS_HPP_ */</span>
</pre></div></div>
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